The inheritance of resistance to Macrophomina phaseolina was determined using traditional approaches and molecular markers. Inheritance studies were based on a cross between the resistant accession BAT-477 and the susceptible accession A-70. Resistance to M. phaseolina was examined by inoculating bean seeds with soil infested with sclerotia of M. phaseolina. The ratio of resistant to susceptible plants in the F2 population was close to 9:7. Bulked segregant analysis identified two random amplified polymorphic DNA (RAPD) markers linked to M. phaseolina resistance. The first RAPD marker (B4591600) was a 1.6-kb band present in the susceptible and absent in the resistant plants. The second RAPD marker (B386900) was a 0.9-kb band present in the resistant, but absent in the susceptible plants. Each of the RAPD markers segregated in a 3:1 ratio as expected, and the segregation of both markers followed a 9:3:3:1 ratio expected for two unlinked loci. In 15 of the 16 F3 families examined, the genotype of the markers correctly predicted the genotype (heterozygous or homozygous) for disease resistance. The one exception could be attributed to recombination between B4591600 and the linked susceptible gene. These data were consistent with the hypothesis that, in BAT-477, resistance to M. phaseolina is controlled by two dominant complementary genes. The symbols Mp-1 and Mp-2 (Macrophomina phaseolina) were proposed for these genes.